libSBML Python API
5.10.0
|
{core}
Abstract Syntax Tree (AST) representation of a mathematical expression.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
Abstract Syntax Trees (ASTs) are a simple kind of data structure used in libSBML for storing mathematical expressions. The ASTNode is the cornerstone of libSBML's AST representation. An AST 'node' represents the most basic, indivisible part of a mathematical formula and come in many types. For instance, there are node types to represent numbers (with subtypes to distinguish integer, real, and rational numbers), names (e.g., constants or variables), simple mathematical operators, logical or relational operators and functions. LibSBML ASTs provide a canonical, in-memory representation for all mathematical formulas regardless of their original format (which might be MathML or might be text strings).
'1 + 2'
is represented as an AST with one plus node having two integer children nodes for the numbers 1
and 2
. The figure also shows the corresponding MathML representation:Infix | AST | MathML |
---|---|---|
1 + 2
|
<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <plus/> <cn type="integer"> 1 </cn> <cn type="integer"> 2 </cn> </apply> </math>
|
The following are other noteworthy points about the AST representation in libSBML:
floatdata
type. This is done so that when an SBML model is read in and then written out again, the amount of change introduced by libSBML to the SBML during the round-trip activity is minimized.For many applications, the details of ASTs are irrelevant because the applications can use the text-string based translation functions such as libsbml.formulaToString(), libsbml.parseL3Formula() and libsbml.parseFormula(). If you find the complexity of using the AST representation of expressions too high for your purposes, perhaps the string-based functions will be more suitable.
Finally, it is worth noting that the AST and MathML handling code in libSBML remains written in C, not C++. (All of libSBML was originally written in C.) Readers may occasionally wonder why some aspects are more C-like and less object oriented, and that's one of the reasons.
AST_.The
list of possible types is quite long, because it covers all the mathematical functions that are permitted in SBML. The values are shown in the following table:AST_CONSTANT_E | AST_FUNCTION_COT | AST_LOGICAL_NOT |
AST_CONSTANT_FALSE | AST_FUNCTION_COTH | AST_LOGICAL_OR |
AST_CONSTANT_PI | AST_FUNCTION_CSC | AST_LOGICAL_XOR |
AST_CONSTANT_TRUE | AST_FUNCTION_CSCH | AST_MINUS |
AST_DIVIDE | AST_FUNCTION_DELAY | AST_NAME |
AST_FUNCTION | AST_FUNCTION_EXP | AST_NAME_AVOGADRO (Level 3 only) |
AST_FUNCTION_ABS | AST_FUNCTION_FACTORIAL | AST_NAME_TIME |
AST_FUNCTION_ARCCOS | AST_FUNCTION_FLOOR | AST_PLUS |
AST_FUNCTION_ARCCOSH | AST_FUNCTION_LN | AST_POWER |
AST_FUNCTION_ARCCOT | AST_FUNCTION_LOG | AST_RATIONAL |
AST_FUNCTION_ARCCOTH | AST_FUNCTION_PIECEWISE | AST_REAL |
AST_FUNCTION_ARCCSC | AST_FUNCTION_POWER | AST_REAL_E |
AST_FUNCTION_ARCCSCH | AST_FUNCTION_ROOT | AST_RELATIONAL_EQ |
AST_FUNCTION_ARCSEC | AST_FUNCTION_SEC | AST_RELATIONAL_GEQ |
AST_FUNCTION_ARCSECH | AST_FUNCTION_SECH | AST_RELATIONAL_GT |
AST_FUNCTION_ARCSIN | AST_FUNCTION_SIN | AST_RELATIONAL_LEQ |
AST_FUNCTION_ARCSINH | AST_FUNCTION_SINH | AST_RELATIONAL_LT |
AST_FUNCTION_ARCTAN | AST_FUNCTION_TAN | AST_RELATIONAL_NEQ |
AST_FUNCTION_ARCTANH | AST_FUNCTION_TANH | AST_TIMES |
AST_FUNCTION_CEILING | AST_INTEGER | AST_UNKNOWN |
AST_FUNCTION_COS | AST_LAMBDA | |
AST_FUNCTION_COSH | AST_LOGICAL_AND |
The types have the following meanings:
'+'
), then the node's type will be AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE, or AST_POWER, as appropriate.AST_FUNCTION_
X, AST_LOGICAL_
X, or AST_RELATIONAL_
X, as appropriate. (Examples: AST_FUNCTION_LOG, AST_RELATIONAL_LEQ.)'ExponentialE'
, 'Pi'
, 'True'
or 'False'
), then the node's type will be AST_CONSTANT_E, AST_CONSTANT_PI, AST_CONSTANT_TRUE, or AST_CONSTANT_FALSE.time
, the value of the node will be AST_NAME_TIME. (Note, however, that the MathML csymbol delay
is translated into a node of type AST_FUNCTION_DELAY. The difference is due to the fact that time
is a single variable, whereas delay
is actually a function taking arguments.)avogadro
, the value of the node will be AST_NAME_AVOGADRO
.The text-string form of mathematical formulas produced bylibsbml.formulaToString() and read bylibsbml.parseFormula() and libsbml.parseL3Formula() are in a simple C-inspired infix notation. A formula in one of these two text-string formats can be handed to a program that understands SBML mathematical expressions, or used as part of a translation system. The libSBML distribution comes with example programs in the 'examples'
subdirectory that demonstrate such things as translating infix formulas into MathML and vice-versa.
Please see the documentation for the functions libsbml.parseFormula() and libsbml.parseL3Formula() for detailed explanations of the infix syntax they accept.
def libsbml.ASTNode.addChild | ( | self, | |
args | |||
) |
Python method signature(s):
addChild(ASTNode self, ASTNode child)int
Adds the given node as a child of this ASTNode.
Child nodes are added in-order, from left to right.
child | the ASTNode instance to add |
def libsbml.ASTNode.addSemanticsAnnotation | ( | self, | |
args | |||
) |
Python method signature(s):
addSemanticsAnnotation(ASTNode self, XMLNode sAnnotation)int
Adds the given XMLNode as a MathML <semantics>
element to this ASTNode.
The <semantics>
element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation>
or <annotation-xml>
elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
sAnnotation | the annotation to add. |
<semantics>
annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.def libsbml.ASTNode.canonicalize | ( | self | ) |
Python method signature(s):
canonicalize(ASTNode self)bool
Converts this ASTNode to a canonical form.
The rules determining the canonical form conversion are as follows:
'ExponentialE'
, 'Pi'
, 'True'
or 'False'
the node type is converted to the corresponding AST_CONSTANT_
X type. AST_FUNCTION_
X or AST_LOGICAL_
X type.SBML Level 1 function names are searched first; thus, for example, canonicalizing log
will result in a node type of AST_FUNCTION_LN. (See the SBML Level 1 Version 2 Specification, Appendix C.)
Sometimes, canonicalization of a node results in a structural conversion of the node as a result of adding a child. For example, a node with the SBML Level 1 function name sqr
and a single child node (the argument) will be transformed to a node of type AST_FUNCTION_POWER with two children. The first child will remain unchanged, but the second child will be an ASTNode of type AST_INTEGER and a value of 2. The function names that result in structural changes are: log10
, sqr
, and sqrt
.
True
if this node was successfully converted to canonical form, False
otherwise. def libsbml.ASTNode.deepCopy | ( | self | ) |
def libsbml.ASTNode.freeName | ( | self | ) |
{core}
Abstract Syntax Tree (AST) representation of a mathematical expression.This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
Abstract Syntax Trees (ASTs) are a simple kind of data structure used in libSBML for storing mathematical expressions. The ASTNode is the cornerstone of libSBML's AST representation. An AST 'node' represents the most basic, indivisible part of a mathematical formula and come in many types. For instance, there are node types to represent numbers (with subtypes to distinguish integer, real, and rational numbers), names (e.g., constants or variables), simple mathematical operators, logical or relational operators and functions. LibSBML ASTs provide a canonical, in-memory representation for all mathematical formulas regardless of their original format (which might be MathML or might be text strings).
'1 + 2'
is represented as an AST with one plus node having two integer children nodes for the numbers 1
and 2
. The figure also shows the corresponding MathML representation:Infix | AST | MathML |
---|---|---|
1 + 2
|
<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <plus/> <cn type="integer"> 1 </cn> <cn type="integer"> 2 </cn> </apply> </math>
|
The following are other noteworthy points about the AST representation in libSBML:
floatdata
type. This is done so that when an SBML model is read in and then written out again, the amount of change introduced by libSBML to the SBML during the round-trip activity is minimized.For many applications, the details of ASTs are irrelevant because the applications can use the text-string based translation functions such as libsbml.formulaToString(), libsbml.parseL3Formula() and libsbml.parseFormula(). If you find the complexity of using the AST representation of expressions too high for your purposes, perhaps the string-based functions will be more suitable.
Finally, it is worth noting that the AST and MathML handling code in libSBML remains written in C, not C++. (All of libSBML was originally written in C.) Readers may occasionally wonder why some aspects are more C-like and less object oriented, and that's one of the reasons.
AST_.The
list of possible types is quite long, because it covers all the mathematical functions that are permitted in SBML. The values are shown in the following table:AST_CONSTANT_E | AST_FUNCTION_COT | AST_LOGICAL_NOT |
AST_CONSTANT_FALSE | AST_FUNCTION_COTH | AST_LOGICAL_OR |
AST_CONSTANT_PI | AST_FUNCTION_CSC | AST_LOGICAL_XOR |
AST_CONSTANT_TRUE | AST_FUNCTION_CSCH | AST_MINUS |
AST_DIVIDE | AST_FUNCTION_DELAY | AST_NAME |
AST_FUNCTION | AST_FUNCTION_EXP | AST_NAME_AVOGADRO (Level 3 only) |
AST_FUNCTION_ABS | AST_FUNCTION_FACTORIAL | AST_NAME_TIME |
AST_FUNCTION_ARCCOS | AST_FUNCTION_FLOOR | AST_PLUS |
AST_FUNCTION_ARCCOSH | AST_FUNCTION_LN | AST_POWER |
AST_FUNCTION_ARCCOT | AST_FUNCTION_LOG | AST_RATIONAL |
AST_FUNCTION_ARCCOTH | AST_FUNCTION_PIECEWISE | AST_REAL |
AST_FUNCTION_ARCCSC | AST_FUNCTION_POWER | AST_REAL_E |
AST_FUNCTION_ARCCSCH | AST_FUNCTION_ROOT | AST_RELATIONAL_EQ |
AST_FUNCTION_ARCSEC | AST_FUNCTION_SEC | AST_RELATIONAL_GEQ |
AST_FUNCTION_ARCSECH | AST_FUNCTION_SECH | AST_RELATIONAL_GT |
AST_FUNCTION_ARCSIN | AST_FUNCTION_SIN | AST_RELATIONAL_LEQ |
AST_FUNCTION_ARCSINH | AST_FUNCTION_SINH | AST_RELATIONAL_LT |
AST_FUNCTION_ARCTAN | AST_FUNCTION_TAN | AST_RELATIONAL_NEQ |
AST_FUNCTION_ARCTANH | AST_FUNCTION_TANH | AST_TIMES |
AST_FUNCTION_CEILING | AST_INTEGER | AST_UNKNOWN |
AST_FUNCTION_COS | AST_LAMBDA | |
AST_FUNCTION_COSH | AST_LOGICAL_AND |
The types have the following meanings:
'+'
), then the node's type will be AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE, or AST_POWER, as appropriate.AST_FUNCTION_
X, AST_LOGICAL_
X, or AST_RELATIONAL_
X, as appropriate. (Examples: AST_FUNCTION_LOG, AST_RELATIONAL_LEQ.)'ExponentialE'
, 'Pi'
, 'True'
or 'False'
), then the node's type will be AST_CONSTANT_E, AST_CONSTANT_PI, AST_CONSTANT_TRUE, or AST_CONSTANT_FALSE.time
, the value of the node will be AST_NAME_TIME. (Note, however, that the MathML csymbol delay
is translated into a node of type AST_FUNCTION_DELAY. The difference is due to the fact that time
is a single variable, whereas delay
is actually a function taking arguments.)avogadro
, the value of the node will be AST_NAME_AVOGADRO
.The text-string form of mathematical formulas produced bylibsbml.formulaToString() and read bylibsbml.parseFormula() and libsbml.parseL3Formula() are in a simple C-inspired infix notation. A formula in one of these two text-string formats can be handed to a program that understands SBML mathematical expressions, or used as part of a translation system. The libSBML distribution comes with example programs in the 'examples'
subdirectory that demonstrate such things as translating infix formulas into MathML and vice-versa.
Please see the documentation for the functions libsbml.parseFormula() and libsbml.parseL3Formula() for detailed explanations of the infix syntax they accept.
freeName(ASTNode self)int
Frees the name of this ASTNode and sets it to None
.
This operation is only applicable to ASTNode objects corresponding to operators, numbers, or AST_UNKNOWN. This method has no effect on other types of nodes.
def libsbml.ASTNode.getCharacter | ( | self | ) |
Python method signature(s):
getCharacter(ASTNode self)string
Returns the value of this node as a single character.
This function should be called only when ASTNode.getType() returns AST_PLUS, AST_MINUS, AST_TIMES, AST_DIVIDE or AST_POWER.
def libsbml.ASTNode.getChild | ( | self, | |
args | |||
) |
Python method signature(s):
getChild(ASTNode self, long n)ASTNode
Returns the child at index n of this node.
n | the index of the child to get |
None
if this node has no nth child (n >
ASTNode.getNumChildren() - 1
).def libsbml.ASTNode.getClass | ( | self | ) |
Python method signature(s):
getClass(ASTNode self)string
Returns the MathML class
attribute value of this ASTNode.
def libsbml.ASTNode.getDefinitionURL | ( | self | ) |
Python method signature(s):
getDefinitionURL(ASTNode self)XMLAttributes
Returns the MathML definitionURL
attribute value.
definitionURL
attribute, in the form of a libSBML XMLAttributes object.def libsbml.ASTNode.getDefinitionURLString | ( | self | ) |
Python method signature(s):
getDefinitionURLString(ASTNode self)string
Returns the MathML definitionURL
attribute value as a string.
definitionURL
attribute, as a string.def libsbml.ASTNode.getDenominator | ( | self | ) |
Python method signature(s):
getDenominator(ASTNode self)long
Returns the value of the denominator of this node.
1
if this node has no numerical value.1
if the node type is another type, but since 1
may be a valid value for the denominator of a rational number, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value. def libsbml.ASTNode.getExponent | ( | self | ) |
Python method signature(s):
getExponent(ASTNode self)long
Returns the exponent value of this ASTNode.
0
if this is not a type of node that has an exponent.0
if the node type is another type, but since 0
may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value. def libsbml.ASTNode.getExtendedType | ( | self | ) |
Python method signature(s):
getExtendedType(ASTNode self)int
Returns the extended type of this ASTNode.
The type may be either a core integer type codeor a value of a type code defined by an SBML Level 3 package.
def libsbml.ASTNode.getId | ( | self | ) |
def libsbml.ASTNode.getInteger | ( | self | ) |
Python method signature(s):
getInteger(ASTNode self)long
Returns the value of this node as an integer.
If this node type is AST_RATIONAL, this method returns the value of the numerator.
long
) integer.0
if the node type is not one of these, but since 0
may be a valid value for integer, it is important to be sure that the node type is one of the expected types in order to understand if 0
is the actual value. def libsbml.ASTNode.getLeftChild | ( | self | ) |
Python method signature(s):
getLeftChild(ASTNode self)ASTNode
Returns the left child of this node.
0
.def libsbml.ASTNode.getListOfNodes | ( | self | ) |
Python method signature(s):
getListOfNodes(ASTNode self)ASTNodeList
Returns an ASTNodeList of all ASTNode objects.
Unlike the equivalent method in the libSBML C/C++ interface, this method does not offer the ability to pass a predicate as an argument. The method always returns the list of all ASTNode objects.
true
(non-zero).def libsbml.ASTNode.getMantissa | ( | self | ) |
Python method signature(s):
getMantissa(ASTNode self)float
Returns the mantissa value of this node.
If ASTNode.getType() returns AST_REAL, this method is identical to ASTNode.getReal().
0
if this node is not a type that has a real-numbered value.0
if the node type is another type, but since 0
may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value. def libsbml.ASTNode.getName | ( | self | ) |
Python method signature(s):
getName(ASTNode self)string *
Returns the value of this node as a string.
This function may be called on nodes that (1) are not operators, i.e., nodes for which ASTNode.isOperator() returns False
, and (2) are not numbers, i.e., ASTNode.isNumber() returns False
.
None
if it is a node that does not have a name equivalent (e.g., if it is a number). def libsbml.ASTNode.getNumChildren | ( | self | ) |
def libsbml.ASTNode.getNumerator | ( | self | ) |
Python method signature(s):
getNumerator(ASTNode self)long
Returns the value of the numerator of this node.
This function should be called only when ASTNode.getType() returns AST_RATIONAL or AST_INTEGER.
def libsbml.ASTNode.getNumSemanticsAnnotations | ( | self | ) |
Python method signature(s):
getNumSemanticsAnnotations(ASTNode self)long
Returns the number of MathML <semantics>
element elements on this node.
The <semantics>
element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation>
or <annotation-xml>
elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
<semantics>
annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.def libsbml.ASTNode.getOperatorName | ( | self | ) |
Python method signature(s):
getOperatorName(ASTNode self)string *
Returns the value of this operator node as a string.
This function may be called on nodes that are operators, i.e., nodes for which ASTNode.isOperator() returns True
.
None
if not an operator). def libsbml.ASTNode.getParentSBMLObject | ( | self | ) |
Python method signature(s):
getParentSBMLObject(ASTNode self)SBase
Returns the parent SBML object.
def libsbml.ASTNode.getPrecedence | ( | self | ) |
Python method signature(s):
getPrecedence(ASTNode self)int
Returns the precedence of this node in the infix math syntax of SBML Level 1.
For more information about the infix syntax, see the discussion about text string formulas at the top of the documentation for ASTNode.
def libsbml.ASTNode.getReal | ( | self | ) |
Python method signature(s):
getReal(ASTNode self)float
Returns the real-numbered value of this node.
This function performs the necessary arithmetic if the node type is AST_REAL_E (mantissa * 10 exponent) or AST_RATIONAL (numerator / denominator).
0
if this is not a node that holds a number.0
if the node type is another type, but since 0
may be a valid value, it is important to be sure that the node type is the correct type in order to correctly interpret the returned value. def libsbml.ASTNode.getRightChild | ( | self | ) |
Python method signature(s):
getRightChild(ASTNode self)ASTNode
Returns the right child of this node.
None
if this node has no right child. If ASTNode.getNumChildren() > 1
, then this is equivalent to: getChild( getNumChildren() - 1 );
def libsbml.ASTNode.getSemanticsAnnotation | ( | self, | |
args | |||
) |
Python method signature(s):
getSemanticsAnnotation(ASTNode self, long n)XMLNode
Returns the nth MathML <semantics>
element on this ASTNode.
The <semantics>
element is a MathML 2.0 construct that can be used to associate additional information with a MathML construct. The construct can be used to decorate a MathML expressions with a sequence of one or more <annotation>
or <annotation-xml>
elements. Each such element contains a pair of items; the first is a symbol that acts as an attribute or key, and the second is the value associated with the attribute or key. Please refer to the MathML 2.0 documentation, particularly the Section 5.2, Semantic Annotations for more information about these constructs.
n | the index of the annotation to return. Callers should use ASTNode.getNumSemanticsAnnotations() to first find out how many annotations there are. |
None
if this node has no nth annotation (n >
ASTNode.getNumSemanticsAnnotations() - 1
).<semantics>
annotation construct, the truth is that this construct has so far (at this time of this writing, which is early 2014) seen very little use in SBML software. The full implications of using these annotations are still poorly understood. If you wish to use this construct, we urge you to discuss possible uses and applications on the SBML discussion lists, particularly sbml-discuss and/or sbml-interoperability.def libsbml.ASTNode.getStyle | ( | self | ) |
Python method signature(s):
getStyle(ASTNode self)string
Returns the MathML style
attribute value of this ASTNode.
def libsbml.ASTNode.getType | ( | self | ) |
Python method signature(s):
getType(ASTNode self)long
Returns the type of this ASTNode.
The value returned is one of the Core AST type codes such as AST_LAMBDA, AST_PLUS, etc.
def libsbml.ASTNode.getUnits | ( | self | ) |
Python method signature(s):
getUnits(ASTNode self)string
Returns the units of this ASTNode.
SBML Level 3 Version 1 introduced the ability to include an attributesbml:units
on MathML cn
elements
appearing in SBML mathematical formulas. The value of this attribute can
be used to indicate the unit of measurement to be associated with the
number in the content of the cn
element. The value of this
attribute must be the identifier of a unit of measurement defined by SBML
or the enclosing Model. Here, the sbml
portion is an XML
namespace prefix that must be associated with the SBML namespace for SBML
Level 3. The following example illustrates how this attribute can be
used to define a number with value 10
and unit of measurement
second
:
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <cn type="integer" sbml:units="second"> 10 </cn> </math>
sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.def libsbml.ASTNode.hasCorrectNumberArguments | ( | self | ) |
Python method signature(s):
hasCorrectNumberArguments(ASTNode self)bool
Returns True
if this ASTNode has the correct number of children for its type.
For example, an ASTNode with type AST_PLUS expects 2 child nodes.
True
if this ASTNode has the appropriate number of children for its type, False
otherwise.def libsbml.ASTNode.hasTypeAndNumChildren | ( | self, | |
args | |||
) |
Python method signature(s):
hasTypeAndNumChildren(ASTNode self, int type, long numchildren)int
Returns True
if this node is of a certain type with a specific number of children.
Designed for use in cases where it is useful to discover if the node is a unary not or unary minus, or a times node with no children, etc.
type | the type of ASTNode sought. |
numchildren | the number of child nodes sought. |
True
if this ASTNode is has the specified type and number of children, False
otherwise. def libsbml.ASTNode.hasUnits | ( | self | ) |
Python method signature(s):
hasUnits(ASTNode self)bool
Returns True
if this node or any of its children nodes have the attribute sbml:units
.
sbml:units
on MathML cn
elements
appearing in SBML mathematical formulas. The value of this attribute can
be used to indicate the unit of measurement to be associated with the
number in the content of the cn
element. The value of this
attribute must be the identifier of a unit of measurement defined by SBML
or the enclosing Model. Here, the sbml
portion is an XML
namespace prefix that must be associated with the SBML namespace for SBML
Level 3. The following example illustrates how this attribute can be
used to define a number with value 10
and unit of measurement
second
:
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <cn type="integer" sbml:units="second"> 10 </cn> </math>
True
if this ASTNode or its children has units associated with it, False
otherwise.sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.def libsbml.ASTNode.insertChild | ( | self, | |
args | |||
) |
Python method signature(s):
insertChild(ASTNode self, long n, ASTNode newChild)int
Inserts the given ASTNode node at a given point in the current ASTNode's list of children.
def libsbml.ASTNode.isAvogadro | ( | self | ) |
Python method signature(s):
isAvogadro(ASTNode self)bool
Returns True
if this node represents the predefined value for Avogadro's constant.
SBML Level 3 introduced a predefined MathML <csymbol>
for the value of Avogadro's constant. LibSBML stores this internally as a node of type AST_NAME_AVOGADRO. This method returns True
if this node has that type.
True
if this ASTNode is the special symbol avogadro, False
otherwise.def libsbml.ASTNode.isBoolean | ( | self | ) |
def libsbml.ASTNode.isConstant | ( | self | ) |
Python method signature(s):
isConstant(ASTNode self)bool
Returns True
if this node represents a MathML constant.
Examples of MathML constants include such things as pi.
True
if this ASTNode is a MathML constant, False
otherwise.True
for nodes of type AST_NAME_AVOGADRO in SBML Level 3. def libsbml.ASTNode.isFunction | ( | self | ) |
Python method signature(s):
isFunction(ASTNode self)bool
Returns True
if this node represents a function.
The three types of functions in SBML are MathML functions (e.g., abs()
), SBML Level 1 functions (in the SBML Level 1 math syntax), and user-defined functions (using FunctionDefinition in SBML Level 2 and 3).
True
if this ASTNode is a function, False
otherwise. def libsbml.ASTNode.isInfinity | ( | self | ) |
def libsbml.ASTNode.isInteger | ( | self | ) |
Python method signature(s):
isInteger(ASTNode self)bool
Returns True
if this node contains an integer value.
True
if this ASTNode is of type AST_INTEGER, False
otherwise. def libsbml.ASTNode.isLambda | ( | self | ) |
Python method signature(s):
isLambda(ASTNode self)bool
Returns True
if this node is a MathML <lambda>
.
True
if this ASTNode is of type AST_LAMBDA, False
otherwise. def libsbml.ASTNode.isLog10 | ( | self | ) |
Python method signature(s):
isLog10(ASTNode self)bool
Returns True
if this node represents a log10
function.
More precisely, this predicate returns True
if the node type is AST_FUNCTION_LOG with two children, the first of which is an AST_INTEGER equal to 10.
True
if the given ASTNode represents a log10()
function, false
otherwise.def libsbml.ASTNode.isLogical | ( | self | ) |
def libsbml.ASTNode.isName | ( | self | ) |
Python method signature(s):
isName(ASTNode self)bool
Returns True
if this node is a user-defined variable name or the symbols for time or Avogadro's constant.
SBML Levels 2 and 3 provides <csymbol>
definitions for 'time' and 'avogadro', which can be used to represent simulation time and Avogadro's constant in MathML.
True
if this ASTNode is a user-defined variable name in SBML or the special symbols for time or Avogadro's constant. It returns false
otherwise. def libsbml.ASTNode.isNaN | ( | self | ) |
def libsbml.ASTNode.isNegInfinity | ( | self | ) |
def libsbml.ASTNode.isNumber | ( | self | ) |
def libsbml.ASTNode.isOperator | ( | self | ) |
def libsbml.ASTNode.isPiecewise | ( | self | ) |
def libsbml.ASTNode.isQualifier | ( | self | ) |
def libsbml.ASTNode.isRational | ( | self | ) |
Python method signature(s):
isRational(ASTNode self)bool
Returns True
if this node represents a rational number.
True
if this ASTNode is of type AST_RATIONAL, false
otherwise. def libsbml.ASTNode.isReal | ( | self | ) |
Python method signature(s):
isReal(ASTNode self)bool
Returns True
if this node can represent a real number.
More precisely, this node must be of one of the following types: AST_REAL, AST_REAL_E or AST_RATIONAL.
True
if the value of this ASTNode can represented as a real number, False
otherwise. def libsbml.ASTNode.isRelational | ( | self | ) |
def libsbml.ASTNode.isSemantics | ( | self | ) |
def libsbml.ASTNode.isSetClass | ( | self | ) |
Python method signature(s):
isSetClass(ASTNode self)bool
Returns True
if this node has a value for the MathML attribute class
.
False
otherwise.def libsbml.ASTNode.isSetId | ( | self | ) |
Python method signature(s):
isSetId(ASTNode self)bool
Returns True
if this node has a value for the MathML attribute id
.
False
otherwise.def libsbml.ASTNode.isSetParentSBMLObject | ( | self | ) |
Python method signature(s):
isSetParentSBMLObject(ASTNode self)bool
Returns True
if this node has a value for the parent SBML object.
False
otherwise.def libsbml.ASTNode.isSetStyle | ( | self | ) |
Python method signature(s):
isSetStyle(ASTNode self)bool
Returns True
if this node has a value for the MathML attribute style
.
False
otherwise.def libsbml.ASTNode.isSetUnits | ( | self | ) |
Python method signature(s):
isSetUnits(ASTNode self)bool
Returns True
if this node has the attribute sbml:units
.
sbml:units
on MathML cn
elements
appearing in SBML mathematical formulas. The value of this attribute can
be used to indicate the unit of measurement to be associated with the
number in the content of the cn
element. The value of this
attribute must be the identifier of a unit of measurement defined by SBML
or the enclosing Model. Here, the sbml
portion is an XML
namespace prefix that must be associated with the SBML namespace for SBML
Level 3. The following example illustrates how this attribute can be
used to define a number with value 10
and unit of measurement
second
:
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <cn type="integer" sbml:units="second"> 10 </cn> </math>
True
if this ASTNode has units associated with it, False
otherwise.sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.def libsbml.ASTNode.isSetUserData | ( | self | ) |
def libsbml.ASTNode.isSqrt | ( | self | ) |
Python method signature(s):
isSqrt(ASTNode self)bool
Returns True
if this node represents a square root function.
More precisely, the node type must be AST_FUNCTION_ROOT with two children, the first of which is an AST_INTEGER node having value equal to 2.
True
if the given ASTNode represents a sqrt()
function, False
otherwise. def libsbml.ASTNode.isUMinus | ( | self | ) |
Python method signature(s):
isUMinus(ASTNode self)bool
Returns True
if this node is a unary minus operator.
A node is defined as a unary minus node if it is of type AST_MINUS and has exactly one child.
For numbers, unary minus nodes can be 'collapsed' by negating the number. In fact, libsbml.parseFormula() does this during its parsing process, and libsbml.parseL3Formula() has a configuration option that allows this behavior to be turned on or off. However, unary minus nodes for symbols (AST_NAME) cannot be 'collapsed', so this predicate function is necessary.
True
if this ASTNode is a unary minus, False
otherwise.def libsbml.ASTNode.isUnknown | ( | self | ) |
Python method signature(s):
isUnknown(ASTNode self)bool
Returns True
if this node has an unknown type.
'Unknown' nodes have the type AST_UNKNOWN. Nodes with unknown types will not appear in an ASTNode tree returned by libSBML based upon valid SBML input; the only situation in which a node with type AST_UNKNOWN may appear is immediately after having create a new, untyped node using the ASTNode constructor. Callers creating nodes should endeavor to set the type to a valid node type as soon as possible after creating new nodes.
True
if this ASTNode is of type AST_UNKNOWN, False
otherwise. def libsbml.ASTNode.isUPlus | ( | self | ) |
def libsbml.ASTNode.isWellFormedASTNode | ( | self | ) |
Python method signature(s):
isWellFormedASTNode(ASTNode self)bool
Returns True
or False
depending on whether this ASTNode is well-formed.
True
if this ASTNode is well-formed, False
otherwise.def libsbml.ASTNode.prependChild | ( | self, | |
args | |||
) |
Python method signature(s):
prependChild(ASTNode self, ASTNode child)int
Adds the given node as a child of this ASTNode.
This method adds child nodes from right to left.
child | the ASTNode instance to add |
def libsbml.ASTNode.reduceToBinary | ( | self | ) |
def libsbml.ASTNode.removeChild | ( | self, | |
args | |||
) |
Python method signature(s):
removeChild(ASTNode self, long n)int
Removes the nth child of this ASTNode object.
n | long the index of the child to remove |
def libsbml.ASTNode.renameSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameSIdRefs(ASTNode self, string oldid, string newid)
Renames all the SIdRef attributes on this node and its child nodes.
oldid | the old identifier. |
newid | the new identifier. |
def libsbml.ASTNode.renameUnitSIdRefs | ( | self, | |
args | |||
) |
Python method signature(s):
renameUnitSIdRefs(ASTNode self, string oldid, string newid)
Renames all the UnitSIdRef attributes on this node and its child nodes.
The only place UnitSIDRefs appear in MathML <cn>
elements, so the effects of this method are limited to that.
oldid | the old identifier. |
newid | the new identifier. |
def libsbml.ASTNode.replaceArgument | ( | self, | |
args | |||
) |
Python method signature(s):
replaceArgument(ASTNode self, string bvar, ASTNode arg)
Replaces occurrences of a given name with a given ASTNode.
For example, if the formula in this ASTNode is x + y
, then the <bvar>
is x
and arg
is an ASTNode representing the real value 3
. This method substitutes 3
for x
within this ASTNode object.
bvar | a string representing the variable name to be substituted. |
arg | an ASTNode representing the name/value/formula to use as a replacement. |
def libsbml.ASTNode.replaceChild | ( | self, | |
args | |||
) |
Python method signature(s):
replaceChild(ASTNode self, long n, ASTNode newChild)int
Replaces the nth child of this ASTNode with the given ASTNode.
n | long the index of the child to replace |
newChild | ASTNode to replace the nth child |
def libsbml.ASTNode.returnsBoolean | ( | self, | |
model = None |
|||
) |
Python method signature(s):
returnsBoolean(ASTNode self, Model model=None)bool returnsBoolean(ASTNode self)
bool
Returns True
if this node returns a Boolean value.
This function looks at the whole ASTNode rather than just the top level of the ASTNode. Thus, it will consider return values from piecewise statements. In addition, if this ASTNode uses a function call to a user-defined function, the return value of the corresponding FunctionDefinition object will be determined. Note that this is only possible where the ASTNode can trace its parent Model; that is, the ASTNode must represent the <math>
element of some SBML object that has already been added to an instance of an SBMLDocument.
model | the Model to use as context |
False
otherwise. def libsbml.ASTNode.setCharacter | ( | self, | |
args | |||
) |
Python method signature(s):
setCharacter(ASTNode self, char value)int
Sets the value of this ASTNode to the given character. If character is one of +
, -
, *
, /
or ^
, the node type will be set accordingly. For all other characters, the node type will be set to AST_UNKNOWN.
value | the character value to which the node's value should be set. |
def libsbml.ASTNode.setClass | ( | self, | |
args | |||
) |
Python method signature(s):
setClass(ASTNode self, string className)int
Sets the MathML attribute class
of this ASTNode.
className | string representing the MathML class for this node. |
def libsbml.ASTNode.setDefinitionURL | ( | self, | |
args | |||
) |
Python method signature(s):
setDefinitionURL(ASTNode self, XMLAttributes url)int setDefinitionURL(ASTNode self, string url)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setDefinitionURL(XMLAttributes url)
Sets the MathML attribute definitionURL
.
url | the URL value for the definitionURL attribute. |
setDefinitionURL(string url)
Sets the MathML attribute definitionURL
.
url | the URL value for the definitionURL attribute. |
def libsbml.ASTNode.setId | ( | self, | |
args | |||
) |
def libsbml.ASTNode.setName | ( | self, | |
args | |||
) |
Python method signature(s):
setName(ASTNode self, char * name)int
Sets the value of this ASTNode to the given name.
As a side effect, this ASTNode object's type will be reset to AST_NAME if (and only if) the ASTNode was previously an operator (i.e., ASTNode.isOperator() returns True
), number (i.e., ASTNode.isNumber() returns True
), or unknown. This allows names to be set for AST_FUNCTION nodes and the like.
name | the string containing the name to which this node's value should be set. |
def libsbml.ASTNode.setStyle | ( | self, | |
args | |||
) |
Python method signature(s):
setStyle(ASTNode self, string style)int
Sets the MathML attribute style
of this ASTNode.
style | string representing the identifier. |
def libsbml.ASTNode.setType | ( | self, | |
args | |||
) |
Python method signature(s):
setType(ASTNode self, long type)int setType(ASTNode self, int type)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setType(int type)
Sets the type of this ASTNode.
This uses integer type codes, which may come from long or an enumeration of AST types in an SBML Level 3 package.
type | the integer representing the type to which this node should be set. |
setType(long type)
Sets the type of this ASTNode to the given type code.
type | the type to which this node should be set. |
def libsbml.ASTNode.setUnits | ( | self, | |
args | |||
) |
Python method signature(s):
setUnits(ASTNode self, string units)int
Sets the units of this ASTNode to units.
The units will be set only if this ASTNode object represents a MathML <cn>
element, i.e., represents a number. Callers may use ASTNode.isNumber() to inquire whether the node is of that type.
sbml:units
on MathML cn
elements
appearing in SBML mathematical formulas. The value of this attribute can
be used to indicate the unit of measurement to be associated with the
number in the content of the cn
element. The value of this
attribute must be the identifier of a unit of measurement defined by SBML
or the enclosing Model. Here, the sbml
portion is an XML
namespace prefix that must be associated with the SBML namespace for SBML
Level 3. The following example illustrates how this attribute can be
used to define a number with value 10
and unit of measurement
second
:
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core"> <cn type="integer" sbml:units="second"> 10 </cn> </math>
units | string representing the unit identifier. |
sbml:units
attribute is only available in SBML Level 3. It may not be used in Levels 1–2 of SBML.def libsbml.ASTNode.setValue | ( | self, | |
args | |||
) |
Python method signature(s):
setValue(ASTNode self, long value)int setValue(ASTNode self, long numerator, long denominator)
int setValue(ASTNode self, float value)
int setValue(ASTNode self, float mantissa, long exponent)
int
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
setValue(long numerator, long denominator)
Sets the value of this ASTNode to the given rational.
As a side effect, this operation sets the node type to AST_RATIONAL.
numerator | the numerator value of the rational. |
denominator | the denominator value of the rational. |
setValue (float mantissa, long exponent)
Sets the value of this ASTNode to the given real (float
)
As a side effet, this operation sets the node type to AST_REAL_E.
mantissa | the mantissa of this node's real-numbered value. |
exponent | the exponent of this node's real-numbered value. |
setValue(int value)
Sets the value of this ASTNode to the given integer
As a side effect, this operation sets the node type to AST_INTEGER.
value | the integer to which this node's value should be set. |
setValue (float value)
Sets the value of this ASTNode to the given real (float
).
As a side effect, this operation sets the node type to AST_REAL.
This is functionally equivalent to:
setValue(value, 0);
value | the float format number to which this node's value should be set. |
setValue(long value)
Sets the value of this ASTNode to the given (long
) integer
As a side effect, this operation sets the node type to AST_INTEGER.
value | the integer to which this node's value should be set. |
def libsbml.ASTNode.swapChildren | ( | self, | |
args | |||
) |
Python method signature(s):
swapChildren(ASTNode self, ASTNode that)int
Swaps the children of this node with the children of another node.
that | the other node whose children should be used to replace this node's children. |
def libsbml.ASTNode.unsetClass | ( | self | ) |
def libsbml.ASTNode.unsetId | ( | self | ) |
def libsbml.ASTNode.unsetParentSBMLObject | ( | self | ) |
Python method signature(s):
unsetParentSBMLObject(ASTNode self)int
Unsets the parent SBML object.
def libsbml.ASTNode.unsetStyle | ( | self | ) |
def libsbml.ASTNode.unsetUnits | ( | self | ) |
def libsbml.ASTNode.unsetUserData | ( | self | ) |
Python method signature(s):
unsetUserData(ASTNode self)int
Unsets the user data of this node.
The user data can be used by the application developer to attach custom information to the node. In case of a deep copy, this attribute will passed as it is. The attribute will be never interpreted by this class.